schrodinger.application.glide.xpdes module

Classes for reading and writing Glide XP Descriptor blocks from pose files.

Copyright Schrodinger LLC. All rights reserved.

schrodinger.application.glide.xpdes.extract_Phob_pack_ligand_indices(data_row)

Returns the ligand indices of the Phob_pack indices data row. The Phob_pack data block contains a row of indices containing [pack value, number of ligand indices, number of protein indices,

lig_0, lig_1, lig_2, …, prot_0, prot_1, prot_2, …]

Note that indices in this data block are zero based, and are incremented here for use in ct atom index access.

Parameters:data_row (list of int) – second row in the Phob_pack data block
Returns:ligand indices in the Phob_pack data block
Return type:list of int
schrodinger.application.glide.xpdes.get_prop(cthandle, dn)

Helper function for m_glide_XPviz_* functions

schrodinger.application.glide.xpdes.get_prop_idx(cthandle, dn, dim)

Helper function for m_glide_XPviz_* functions

schrodinger.application.glide.xpdes.m_glide_XPviz_hbonds(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_phobcon_hb(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_hexsp(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_phobpack(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_stacking(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_rotbonds(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_watmol(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_hexpairs(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_exposure(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penal_blkpchg(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_water_ligand(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penal_polar(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_water_protein(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penal_ddpen(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penal_twistam(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penal_charge(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_penalties(cthandle)
schrodinger.application.glide.xpdes.m_glide_XPviz_picat(cthandle)
class schrodinger.application.glide.xpdes.TermKeywords

Bases: str, enum.Enum

XP-descriptor term keywords. Note that members of this enum may be compared to bare strings.

Molecule = 'Molecule'
H_bonds = 'H_bonds'
Phob_pack = 'Phob_pack'
Hex_pairs = 'Hex_pairs'
Penalties = 'Penalties'
Phobcon_HB = 'Phobcon_HB'
Picat = 'Picat'
Exposure = 'Exposure'
Rot_bonds = 'Rot_bonds'
Hex_sp = 'Hex_sp'
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('Molecule', <TermKeywords.Molecule: 'Molecule'>), ('H_bonds', <TermKeywords.H_bonds: 'H_bonds'>), ('Phob_pack', <TermKeywords.Phob_pack: 'Phob_pack'>), ('Hex_pairs', <TermKeywords.Hex_pairs: 'Hex_pairs'>), ('Penalties', <TermKeywords.Penalties: 'Penalties'>), ('Phobcon_HB', <TermKeywords.Phobcon_HB: 'Phobcon_HB'>), ('Picat', <TermKeywords.Picat: 'Picat'>), ('Exposure', <TermKeywords.Exposure: 'Exposure'>), ('Rot_bonds', <TermKeywords.Rot_bonds: 'Rot_bonds'>), ('Hex_sp', <TermKeywords.Hex_sp: 'Hex_sp'>)]))
__module__ = 'schrodinger.application.glide.xpdes'
class schrodinger.application.glide.xpdes.XpPVParser(filename)

Bases: object

Class for parsing a PV file with XP-descriptor information

__init__(filename)

Read PV file and create a table of XP Descriptor terms

parseBlock_SL(ctnum)

XP parsing for single-ligand scoring. Given ctnum, get and parse XP block return an array of tuples. tuple[0] is an atom number and tuple[1] is the corresponding XP score for that atom Added: tuple[2] the energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.

parseBlock_F(ctnum, st)

XP parsing for fragment scoring. Use st argument to determine the number of rings associated with a set of atoms. Given ctnum, get and parse XP block return an array of tuples containing energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.

Each entry = (atom number, XP score, energy type property)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.glide.xpdes', '__doc__': '\n Class for parsing a PV file with XP-descriptor information\n ', '__init__': <function XpPVParser.__init__>, 'parseBlock_SL': <function XpPVParser.parseBlock_SL>, 'parseBlock_F': <function XpPVParser.parseBlock_F>, '__dict__': <attribute '__dict__' of 'XpPVParser' objects>, '__weakref__': <attribute '__weakref__' of 'XpPVParser' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.glide.xpdes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)